Couple of clarification questions. Do civilian hangars reload box launchers? I don't expect that they do, but it does need clearing up.
Also, can you nest things inside hangars? Could I, for instance, build an auxiliary carrier, and then put a bunch of small military hangars inside it, and fill them with fighters?
And the auxiliary carrier could be quite useful in a couple of ways. The first thing that springs to mind is moving FACs and other small, fast, jump drive-less craft around non-tactically. There's no need for maintainence, as they don't normally deploy from the carrier, and it's cheaper in fuel and logistical headaches. Another would be carrying convoy escorts which have military engines and thus can't use civilian jump drives. Even an FAC-carrier might be of some use when paired with a maintainence ship. But over all, I can't see any of these displacing normal fleet units as the way of the future.